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- PDB-7s11: Crystal structure of Fab in complex with mouse CD96 monomer -

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Basic information

Entry
Database: PDB / ID: 7s11
TitleCrystal structure of Fab in complex with mouse CD96 monomer
Components
  • Fab heavy chain
  • Fab light chain
  • T-cell surface protein tactile
KeywordsIMMUNE SYSTEM / Immunoglobulin / checkpoint / antibody / complex
Function / homology
Function and homology information


negative regulation of natural killer cell cytokine production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of type II interferon production / cell-matrix adhesion / response to lipopolysaccharide / membrane / cytoplasm
Similarity search - Function
T-cell surface protein tactile / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface protein tactile
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus (rats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLee, P.S. / Chau, B. / Strop, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2021
Title: Antibody blockade of CD96 by distinct molecular mechanisms.
Authors: Lee, P.S. / Chau, B. / Barman, I. / Bee, C. / Jashnani, A. / Hogan, J.M. / Aguilar, B. / Dollinger, G. / Rajpal, A. / Strop, P.
History
DepositionAug 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: T-cell surface protein tactile
H: Fab heavy chain
L: Fab light chain
D: T-cell surface protein tactile
I: Fab heavy chain
M: Fab light chain
E: T-cell surface protein tactile
J: Fab heavy chain
N: Fab light chain
F: T-cell surface protein tactile
K: Fab heavy chain
O: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,72920
Polymers245,71012
Non-polymers1,0198
Water00
1
C: T-cell surface protein tactile
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8416
Polymers61,4283
Non-polymers4133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: T-cell surface protein tactile
I: Fab heavy chain
M: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8416
Polymers61,4283
Non-polymers4133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: T-cell surface protein tactile
J: Fab heavy chain
N: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5244
Polymers61,4283
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: T-cell surface protein tactile
K: Fab heavy chain
O: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5244
Polymers61,4283
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.930, 154.890, 306.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "C" and (resid 30 through 94 or resid 101 through 137))
d_2ens_1(chain "D" and (resid 30 through 94 or resid 101 through 137))
d_3ens_1chain "F"
d_1ens_2(chain "H" and (resid 2 through 126 or resid 131 through 214))
d_2ens_2chain "I"
d_3ens_2(chain "J" and (resid 2 through 126 or resid 131 through 214))
d_4ens_2(chain "K" and (resid 2 through 126 or resid 131 through 214))
d_1ens_3(chain "L" and (resid 1 through 165 or resid 170 through 212))
d_2ens_3(chain "M" and resid 1 through 212)
d_3ens_3(chain "N" and (resid 1 through 165 or resid 167 through 168 or resid 172 through 212))
d_4ens_3(chain "O" and (resid 1 through 165 or resid 167 through 212))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYTHRA6 - 70
d_12ens_1TRPGLUA77 - 113
d_21ens_1GLYTHRE6 - 70
d_22ens_1TRPGLUE77 - 113
d_31ens_1GLYGLUL1 - 102
d_11ens_2VALPROC1 - 130
d_12ens_2THRLYSC135 - 218
d_21ens_2VALLYSG1 - 214
d_31ens_2VALPROJ1 - 130
d_32ens_2THRLYSJ135 - 218
d_41ens_2VALPROM1 - 130
d_42ens_2THRLYSM135 - 218
d_11ens_3PCAGLUD1 - 167
d_12ens_3ASPGLYD169 - 211
d_21ens_3PCAGLYH1 - 210
d_31ens_3PCAGLUK1 - 167
d_32ens_3ASPSERK169 - 170
d_33ens_3THRGLYK174 - 214
d_41ens_3PCAGLUN1 - 167
d_42ens_3ASPGLYN169 - 211

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.882443740463, -0.464521773707, 0.074246661005), (0.465650564718, -0.884965522069, -0.00236142474966), (0.0668026683314, 0.0324891751365, 0.997237111726)84.6187845173, 39.4790361151, -37.6469461297
2given(0.178169197397, -0.41851186843, -0.890563615404), (-0.373854226774, -0.865969440505, 0.332159517754), (-0.910213576158, 0.273760377144, -0.310751511153)104.063063211, 17.8538671247, 184.359339005
3given(-0.865954982841, -0.498935199783, 0.0344330380673), (0.49920400616, -0.8664840105, -0.000905418206823), (0.0302874219322, 0.0164050591397, 0.99940659699)88.7619620472, 36.9756925739, -35.1171247935
4given(0.145941395176, 0.881413834106, 0.449233527489), (0.321433382476, 0.387210782735, -0.864146046895), (-0.935618346231, 0.270513331982, -0.226805748198)-85.2718492901, 58.9827845666, 140.644067445
5given(0.124043082867, -0.505403843544, -0.853920528225), (-0.447797257152, -0.796465516215, 0.406349969814), (-0.885489090887, 0.331978367386, -0.325114492921)106.288791226, 11.6920367693, 182.417485146
6given(-0.886026343343, -0.462946659283, 0.0252529119477), (0.46246934223, -0.886346686831, -0.0226198638819), (0.0328546252552, -0.00836309770439, 0.999425150872)88.816752442, 41.5562061237, -33.8467250876
7given(0.213120253121, 0.836884657523, 0.504186302583), (0.359625218832, 0.412618724523, -0.836908292559), (-0.90843241889, 0.359680216547, -0.213027421087)-91.583744067, 54.0521940853, 133.062836709
8given(0.0977020085566, -0.484856032631, -0.869119637993), (-0.456028758721, -0.798031394211, 0.393933579519), (-0.88458582893, 0.357855447737, -0.299077564825)107.66635124, 13.5030977058, 177.951015408

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Components

#1: Protein
T-cell surface protein tactile / Cell surface antigen CD96 / T cell-activated increased late expression protein


Mass: 13904.558 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd96 / Production host: Homo sapiens (human) / References: UniProt: Q3U0X8
#2: Antibody
Fab heavy chain


Mass: 24474.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rats) / Production host: Homo sapiens (human)
#3: Antibody
Fab light chain


Mass: 23048.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rats) / Production host: Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M ammonium sulfate, 0.1 M bis-tris pH 5.5, 1% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→153 Å / Num. obs: 59695 / % possible obs: 88.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 55.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.082 / Net I/σ(I): 6.6
Reflection shellResolution: 2.58→2.96 Å / Rmerge(I) obs: 1.422 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2986 / CC1/2: 0.545 / Rpim(I) all: 0.596

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MJ8, 4AMK, 6ARQ

3mj8

4amk

6arq


Resolution: 2.58→61.2 Å / SU ML: 0.333 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 2923 4.9 %
Rwork0.2258 56745 -
obs0.2284 59668 63.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.91 Å2
Refinement stepCycle: LAST / Resolution: 2.58→61.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16225 0 58 0 16283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014116634
X-RAY DIFFRACTIONf_angle_d2.114622657
X-RAY DIFFRACTIONf_chiral_restr0.09662628
X-RAY DIFFRACTIONf_plane_restr0.0192864
X-RAY DIFFRACTIONf_dihedral_angle_d8.87982277
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS1.37361640076
ens_1d_3FX-RAY DIFFRACTIONTorsion NCS1.85415635645
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.07888255158
ens_2d_3CX-RAY DIFFRACTIONTorsion NCS1.74144043295
ens_2d_4CX-RAY DIFFRACTIONTorsion NCS1.22509178968
ens_3d_2DX-RAY DIFFRACTIONTorsion NCS1.01558419689
ens_3d_3DX-RAY DIFFRACTIONTorsion NCS1.79243113646
ens_3d_4DX-RAY DIFFRACTIONTorsion NCS1.2654481862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.620.02920.408837X-RAY DIFFRACTION0.89
2.62-2.670.353190.3408176X-RAY DIFFRACTION4.26
2.67-2.710.4379270.3514439X-RAY DIFFRACTION10.67
2.71-2.770.4068290.3718811X-RAY DIFFRACTION18.77
2.77-2.820.3287550.33931125X-RAY DIFFRACTION26.91
2.82-2.880.3797780.34621597X-RAY DIFFRACTION38.06
2.88-2.950.35681050.3432068X-RAY DIFFRACTION49.39
2.95-3.020.37851430.32962578X-RAY DIFFRACTION61.16
3.02-3.110.35831380.3232971X-RAY DIFFRACTION70.43
3.11-3.20.31661520.31283291X-RAY DIFFRACTION77.58
3.2-3.30.34941850.29223616X-RAY DIFFRACTION85.82
3.3-3.410.31011870.27833592X-RAY DIFFRACTION90.45
3.48-3.560.3716990.26072075X-RAY DIFFRACTION93.99
3.56-3.720.3312190.24783690X-RAY DIFFRACTION88.32
3.72-3.910.34261300.24452884X-RAY DIFFRACTION67.81
3.91-4.160.25582030.20974291X-RAY DIFFRACTION99.96
4.16-4.480.23522460.17674207X-RAY DIFFRACTION99.96
4.48-4.930.22422310.16914259X-RAY DIFFRACTION99.98
4.93-5.640.24352010.19184300X-RAY DIFFRACTION99.98
5.64-7.110.28852490.23134312X-RAY DIFFRACTION100
7.11-61.20.23552350.19084426X-RAY DIFFRACTION99.3
Refinement TLS params.Method: refined / Origin x: 19.4043462483 Å / Origin y: 14.5156127787 Å / Origin z: 103.558449099 Å
111213212223313233
T0.273580952441 Å2-0.00167415248905 Å2-0.0609167957404 Å2-0.304988580524 Å2-0.012881836607 Å2--0.237625645223 Å2
L0.129339568963 °20.0822412874673 °2-0.14375624018 °2-0.12119594993 °2-0.0753589266367 °2--0.0246991371431 °2
S0.0264366880456 Å °-0.0417472320888 Å °0.0191560894383 Å °0.0792545731217 Å °-0.0142739071358 Å °-0.0021636182979 Å °-0.0572574371358 Å °-0.0391998082606 Å °-0.00568487173086 Å °
Refinement TLS groupSelection details: all

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